7Z16 | pdb_00007z16

E. coli C-P lyase bound to PhnK/PhnL dual ABC dimer with AMPPNP and PhnK E171Q mutation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural remodelling of the carbon-phosphorus lyase machinery by a dual ABC ATPase.

Amstrup, S.K.Ong, S.C.Sofos, N.Karlsen, J.L.Skjerning, R.B.Boesen, T.Enghild, J.J.Hove-Jensen, B.Brodersen, D.E.

(2023) Nat Commun 14: 1001-1001

  • DOI: https://doi.org/10.1038/s41467-023-36604-y
  • Primary Citation Related Structures: 
    7Z15, 7Z16, 7Z17, 7Z18, 7Z19

  • PubMed Abstract: 

    In Escherichia coli, the 14-cistron phn operon encoding carbon-phosphorus lyase allows for utilisation of phosphorus from a wide range of stable phosphonate compounds containing a C-P bond. As part of a complex, multi-step pathway, the PhnJ subunit was shown to cleave the C-P bond via a radical mechanism, however, the details of the reaction could not immediately be reconciled with the crystal structure of a 220 kDa PhnGHIJ C-P lyase core complex, leaving a significant gap in our understanding of phosphonate breakdown in bacteria. Here, we show using single-particle cryogenic electron microscopy that PhnJ mediates binding of a double dimer of the ATP-binding cassette proteins, PhnK and PhnL, to the core complex. ATP hydrolysis induces drastic structural remodelling leading to opening of the core complex and reconfiguration of a metal-binding and putative active site located at the interface between the PhnI and PhnJ subunits.


  • Organizational Affiliation
    • Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark.

Macromolecule Content 

  • Total Structure Weight: 331.85 kDa 
  • Atom Count: 22,450 
  • Modeled Residue Count: 2,882 
  • Deposited Residue Count: 2,992 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphonate C-P lyase system protein PhnG
A, E
150Escherichia coliMutation(s): 0 
Gene Names: phnGI6H00_16560
EC: 2.7.8.37
UniProt
Find proteins for P16685 (Escherichia coli (strain K12))
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UniProt GroupP16685
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH
B, F
194Escherichia coliMutation(s): 0 
Gene Names: phnHb4100JW4061
EC: 2.7.8.37
UniProt
Find proteins for P16686 (Escherichia coli (strain K12))
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UniProt GroupP16686
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI
C, G
354Escherichia coliMutation(s): 0 
Gene Names: 
EC: 2.7.8.37
UniProt
Find proteins for P16687 (Escherichia coli (strain K12))
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UniProt GroupP16687
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase
D, H
281Escherichia coliMutation(s): 0 
Gene Names: 
phnJA6583_09960A8C65_01335A8X68_003177ABE90_013675ABT96_003416ACN68_27220ACN81_06055ACW72_002453AM340_04020AMK64_003176AO169_002527B2D52_003427B5N24_002958B6L15_003343BANRA_00673BANRA_05179BE930_16685BE963_11965BKD45_002102BMT91_23195BN17_40761BOH76_03140BON63_06820BON70_15410BvCmsHHP019_00759BvCmsHHP056_01954BvCmsKKP005_04467BvCmsKKP057_05062BZL69_05300C6B13_11205C6N50_000781C7B02_13575CBT22_003266CCV12_000642CCZ91_003352CDL57_06200CLG78_001793CS116_003895D3O91_17845D9F92_14655D9H13_21630D9H94_23375D9J03_04665DAH18_16675DAH34_17870DEN89_17230DEO15_07445DIV22_19485DTM45_21575DU321_10015DXT73_06970E2127_04980E2128_22940E2129_04390E5S38_10055E5S47_14750E5S52_04755E5S62_09390EC95NR1_03700ED648_09835EIA08_14550EIA13_06810EKI52_13355ELT17_04080ELT21_01245ELU85_16580ELV10_08795ELY05_00935ERS085366_02412ETECE36_05287F9407_18430FC554_11560G3813_002183G5603_09230GF699_23185GKE84_02440GKF52_14440GLW94_09675GNO40_10425GP650_09635GP954_07790GQE64_23580GQM04_25240GQM09_07635GSY44_18815GUC01_08575GW978_22970HH411_003332HIF90_002933HIR12_003887HJQ60_002653HL425_11400HL601_13475HLZ20_11475HMJ82_12545HND12_12285HNV65_03620HNV94_11935HVZ33_22655I6H02_16305IA00_001785JE86ST02C_46280JE86ST05C_46410NCTC10974_05189NCTC11181_01834NCTC13148_04573NCTC13216_02229NCTC8960_02155NCTC9036_04503NCTC9706_01879PU06_23450RG28_25905UN91_05940WP4S18E08_42000

EC: 4.7.1.1
UniProt
Find proteins for P16688 (Escherichia coli (strain K12))
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UniProt GroupP16688
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative phosphonates utilization ATP-binding protein PhnK
I, J
291Escherichia coliMutation(s): 1 
Gene Names: phnKb4097JW5727
UniProt
Find proteins for P16678 (Escherichia coli (strain K12))
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UniProt GroupP16678
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL
K, L
226Escherichia coliMutation(s): 0 
Gene Names: phnLb4096JW4057
EC: 2.7.8.37
UniProt
Find proteins for P16679 (Escherichia coli (strain K12))
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
(Subject of Investigation/LOI)

Query on ANP



Download:Ideal Coordinates CCD File
T [auth I],
V [auth J]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
O [auth D],
R [auth H]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN

Query on ZN



Download:Ideal Coordinates CCD File
M [auth C],
N [auth D],
P [auth G],
Q [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
S [auth I],
U [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF18OC0030646

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2023-03-08
    Changes: Database references, Refinement description
  • Version 1.2: 2024-07-17
    Changes: Data collection, Refinement description